Dr Schmitz joined James Cook University in July 2021. He is an Associate Professor in Bioinformatics at the Department of Molecular & Cell Biology (CPHMVS) and an NHMRC Emerging Leadership Fellow (2021-2025).

Ulf completed his PhD at the University of Rostock (Germany). In 2015, he joined the Centenary Institute in Sydney as a post-doctoral Research Officer in the Gene and Stem Cell Therapy Program. He later established the Computational Biomedicine Lab at the Centenary. He also holds an appointment as Conjoint Senior Lecturer at the University of Sydney (Faculty of Medicine & Health). 

Ulf is a computational biologist with training in bioinformatics and systems biology and more than 12 years of experience in analysing post-transcriptional gene regulation. His research interests focus on computational RNA biology and Systems Medicine. Ulf and his team develop integrative workflows combining various computational disciplines with experimentation to address questions around non-coding RNAs, post-transcriptional gene regulation, and cancer biology. He has published >50 research articles, 10 book chapters, and 4 books on this topic. 



Available HDR Student Projects

Portable long-read sequencing to diagnose Chronic Kidney Disease

Determining cellular gene isoform abundance from long-read RNA sequencing data

Mirtron synthesis and expression in leukemia

Alternative splicing-based subtyping of 5k leukaemia and lymphoma samples

Single-cell multi-omics data analysis to elucidate gene isoform regulation in Acute Myeloid Leukemia

Developing a web-tool for animal sequencing data analysis


Computational Biomedicine Lab

In the Computational Biomedicine Lab at James Cook University and the Centenary Institute (University of Sydney) computational biologists work hand-in-hand with molecular biologists integrating in silicoin vitro and in vivo approaches in advanced interdisciplinary research. We develop integrative systems medicine workflows along with tools and databases to identify and study interactions between RNAs and other molecules, functional mechanisms of gene regulation, cell signalling pathways and gene regulatory networks.

Our goal is to achieve a deeper understanding of processes involved in disease emergence and progression, with a focus on cancer biology, and possible avenues for therapeutic interventions and optimised treatment schedules. Most projects involve the analysis of experimental high-throughput data (incl. (sc)RNA-seq, NanoString, DNA Methyl-Seq, ChIP-Seq, CLIP-seq, and more). Moreover, we use various mathematical formalisms to model the effects of environmental stimuli or pathogenic events on molecular interaction networks and signalling pathways. Using machine learning and computer simulation approaches, we predict disease progression and outcome as well as the effect of therapeutic agents on cellular survival and resistance mechanisms. 

Current Research Projects

Alternative splicing and the epigenome in Chronic Myeloid Leukaemia

In this project, we are investigating gene regulatory processes in leukaemia. The third biggest cause of cancer death in all Australians is blood cancers (leukaemia), which are diagnosed 35 times each day. Using a multi-omics approach, we examine alternative splicing and epigenetic changes in blood samples from chronic myeloid leukaemia (CML) patients before and after treatment with tyrosine kinase inhibitors. Find out more: Schmitz et al, Cancers 2020


Cooperating microRNAs for cancer therapy

In this project, we use a systems medicine approach to find new avenues for overcoming chemotherapy resistance in aggressive tumour cells. Our results suggest that pairs of cooperating microRNAs could be used as potential RNA therapeutics to reduce E2F1-related chemoresistance. Find out more: Lai X, Gupta SK, Schmitz U et al, Theranostics 2018



Intron retention regulation in haematopoietic cells

There is growing evidence that alternative splicing, including intron retention (IR), is regulated on at least two levels: locally, through a network of interacting trans-acting splicing regulators with cis-acting regulatory elements, and globally, through the chromatin structure. In this project, we explore a global regulation of IR in haematopoietic cells – we use statistical analysis to better understand IR regulation using information derived from the epigenetic factors that govern chromatin organisation, namely nucleosome assembly, DNA methylation, and histone modifications. The main challenge here is to integrate multiple layers of ‘-omics’ into a single computational model which produces biologically interpretable results. Find out more: Petrova et al, bioRxiv 2021



Cross-talk between post-transcriptional gene regulation mechanisms

Combining computational predictions and in vitro assays, we elucidate the cross-talk between post-transcriptional gene regulation mechanisms. More specifically, we focus on interactions between microRNA molecules and intron-retaining mRNA transcripts and try to identify networks of interconnected gene regulation. Using a systems biology approach we will model competitive post-transcriptional gene regulation through iterative cycles of time-course experiments and model simulations.


Portable long-read sequencing to diagnose Chronic Kidney Disease


MicroRNAs as Cancer Biomarkers

  • BC3202: Special Topics in Biochemistry and Molecular Biology (Level 3; TSV)
  • BC3203: Bioinformatics (Level 3; TSV)
  • BC5203: Advanced Bioinformatics (Level 5; TSV)
  • Mentoring Early Career Researchers
  • RNA Biology
  • Cancer Biology
  • Bioinformatics
  • Systems Biology
  • 2021 to present - A/Prof, James Cook University (Townsville/Australia)
  • 2018 to present - Associate Faculty, Centenary Institute (Sydney/Australia)
  • 2015 to present - Conjoint Senior Lecturer, University of Sydney (Australia)
  • 2018 to 2021 - Senior Research Officer, Centenary Institute (Sydney/Australia)
  • 2018 to 2021 - Lab Head, Centenary Institute (Sydney/Australia)
  • 2015 to 2017 - Research Officer, Centenary Institute (Sydney/Australia)
  • 2003 to 2015 - Systems Engineer, University of Rostock (Germany)
Socio-Economic Objectives
  • 2020 - Travel Award - The CASS Foundation
  • 2020 - Centenary Recognition Award for Contribution to Centenary Life
  • 2016 - Cure the Future Award of Scientific Excellence, Cure the Future Foundation
  • 2016 - Joachim-Jungius Award for best PhD thesis at the University of Rostock, Germany
  • 2021 to 2025 - NHMRC Investigator (EL1)
  • 2018 to 2020 - Cancer Institute NSW Early Career Fellowship
  • 2018 to 2019 - Australia-India Strategic Research Fund (AISRF) Early and Mid-Career Fellowship, Australian Academy of Science
  • 2017 to 2019 - NHMRC Peter Doherty Fellowship for Early Career Researchers
  • 2017 - Honorary Adjunct Professorship at Chhattisgarh Swami Vivekanand Technical University (CSVTU), Bhilai, India
  • 2016 - Conjoint Senior Lecturer, Sydney Medical School, University of Sydney

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles
Book Chapters

ResearchOnline@JCU stores 38+ research outputs authored by A/PROF Ulf Schmitz from 2015 onwards.

Current Funding

Current and recent Research Funding to JCU is shown by funding source and project.

National Health & Medical Research Council - Investigator Grants

Investigating post-transcriptional gene regulation in cancer

Indicative Funding
$577,910 over 4 years
In this project we willl employ integrative systems medicine approaches to generate a detailed mechanistic overview of multi-level cancer gene regulation and provide novel avenues for the treatment of aggressive tumours. We will determine patterns of gene regulation in leukaemia and test whether these patterns are predictive for disease outcome. We will devise strategies for the therapeutic interference with gene regulation to effectively sensitise aggressive tumours to chemotherapy and thereby diminish tumour cell populations and prevent relapse.
Ulf Schmitz (College of Public Health and Medical & Vet Sciences)
Bioinformatics; Breast Cancer; Gene Regulation; Computational Biology; Leukaemia; RNA biology

Tour de Cure - PhD Scholarship

Precision Hepatocellular Carcinoma Treatment Using Synthetic Lethality

Indicative Funding
$10,000 over 1 year
Hepatocellular carcinoma (HCC) is a major cause of cancer-related mortality. Current therapies for HCC show little efficacy due to extensive heterogeneity in the disease and a lack of corresponding patient-tailored treatment options. The purpose of this project is to validate various bioinformatic approaches to identifying personalised cancer driver genes and methods of targeting them through synthetic lethality. An integrated pipeline will be developed for the simple identification of therapeutics from sequencing of tissue biopsies. Finally, patient-derived organoids matched with patient-specific sequencing information will be used to validate this pipeline, building an important foundation for the future of personalised treatment.
Rhys Gillman, Lionel Hebbard, Matt Field and Ulf Schmitz (College of Public Health and Medical & Vet Sciences)
Liver Cancer; Genetics; Synthetic Lethality; Bioinformatics; Precision Medicine

Tropical Australian Academic Health Centre Limited - Research Seed Grants

Using portable long-read sequencing to diagnose Chronic Kidney Disease in regional North QLD Using portable long-read sequencing to diagnose Chronic Kidney Disease in regional North Using portable long-read sequencing to diagnose Chronic Kidney Disease

Indicative Funding
$50,000 over 2 years
This project addresses the early diagnosis of genetic predispositions for Chronic Kidney Disease (CKD), which poses an increasing burden on the North Queensland population and unequally affects the Indigenous Australian peoples. We will develop a mobile diagnostic pipeline that allows a rapid and cost-efficient screening for genetic CKD predispositions and circulating biomarkers using a targeted, DNA/RNA long-read sequencing approach.
Ulf Schmitz, Andrew Mallett, Matt Field, Paul Horwood, Helen Wright, Chirag Patel, Ira Cooke and Ben Lundie (College of Public Health, Medical & Vet Sciences, College of Medicine & Dentistry, College of Healthcare Sciences, Queensland Clinical Genetics Service and Pathology Queensland)
long-read sequencing; Nanopore; Chronic Kidney Disease; Genetic Testing; targeted sequencing; transcriptomic complexity

Cancer Council NSW - Project Grants

Deciphering cancer gene regulation

Indicative Funding
$404,943 over 4 years
In this project, we investigate regulatory processes in cancer, whereby the control of protein generation from DNA genetic code is disrupted. This process is referred to as intron retention (IR), a phenomenon, which allows ?junk? DNA to enter the cell. IR plays a critical role in cancer development, yet the mechanism of its involvement remains unresolved. We hypothesise that IR can significantly interfere with other forms of gene regulation via `cross-talk?. This introduces a distortion of gene regulation, which is amenable to therapeutic manipulation. Our enhanced understanding of gene-regulatory cross-talk will facilitate improved IR-directed therapies.
Ulf Schmitz and Charles Bailey (College of Public Health, Medical & Vet Sciences and Centenary Institute of Cancer Medicine & Cell Biology)
Bioinformatics; Breast Cancer; Gene Regulation; Computational Biology; Leukaemia; RNA biology

Advisory Accreditation: I can be on your Advisory Panel as a Primary or Secondary Advisor.

These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

  • Targeting DNA Repair in HCC through Synthetic Lethality (PhD , Secondary Advisor)
  • Immune signatures of inflammatory lung disease (PhD , Secondary Advisor)
  • Analysing the role of chimeric transcripts in human cancers (PhD , Primary Advisor/AM/Adv)
  • Insights into the molecular bases of coral-specific traits (PhD , Secondary Advisor)
  • Pharmacogenomic Profiling of Mental Health Patients in the Philippine National Center for Mental Health (PhD , Secondary Advisor)
  • Investigating monocyte and NK derived MS genes by scSequencing, flow cytometry and cytotoxicity assays. (PhD , Secondary Advisor)

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.

  • 5+ collaborations
  • 4 collaborations
  • 3 collaborations
  • 2 collaborations
  • 1 collaboration
  • Indicates the Tropics (Torrid Zone)

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